Your overall thought process seems correct. I suspect you still have a web
process for galaxy that is the only process being proxied by apache?
Make sure your universe_wsgi.ini has the option set to manage jobs in the
database (required for multiple handlers).
I would start with 8 handlers and work my way up (despite the python GIC
issue). I suspect that each handler with 4 threads would easily saturate your
24 core server.
I believe you need to set the default attribute and the tags attribute (I could
be mistaken).
Here's what I have and it seems to work as expected (please correct it if it's
wrong)
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<destinations default="biocluster">
<!-- Executes jobs on the biocluster | this is the default -->
<destination id="biocluster" runner="drmaa">
<param id="nativeSpecification">-q all.q -S
/bin/bash</param>
</destination>
<!-- Executes job locally on the galaxy host server -->
<destination id="local" runner="local"/>
</destinations>
<handlers default="handlers">
<handler id="handler0" tags="handlers"/>
<handler id="handler1" tags="handlers"/>
<handler id="handler2" tags="handlers"/>
</handlers>
<tools>
<tool id="upload1" destination="local"/>
</tools>
</job_conf>
Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel [email protected]
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Shrum, Donald C
Sent: Tuesday, July 22, 2014 10:24 AM
To: [email protected]
Subject: [galaxy-dev] handlers
I could use a little bit of help in making some changes to our galaxy server.
I'm in the process of setting up/testing a production galaxy server for our
research computing center. Our server is setup with an apache proxy, ldap
authentication and jobs will run as the logged in user.
The server running galaxy has 24 cores. While most of the jobs submitted will
go to either our HPC or the condor cluster there are some jobs that are small
and should run on the galaxy server itself.
I was planning to set up a single web handler and 23 job handlers. I don't
expect the web server to get bogged down, especially since I have apache
serving as a proxy.
I expect a smaller (<100) number of users submitting many jobs.
I just went with 23 handlers for no good reason other than the server has 24
cores. Perhaps there is a better way to discern the optimum number of job
handlers.
I'd like jobs submitted to galaxy to go either to our HPC, Condor, or one of
the 23 local workers. Can galaxy effectively load balance itself in this way?
Does the configuration below accomplish this?
universe_wsgi.ini:
[server:handler1]
use = egg:Paste#http
port = 8081
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10
.
.
[server:handler23]
job_conf.xml:
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" /> <plugin id="drmaa"
type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" /> </plugins>
<handlers> <handler id="handler1"/> ...
<handler id="handler23"/>
</handlers>
<destinations default="dynamic">
<destination id="local" runner="local" tags="head"/> <destination id="dynamic"
runner="dynamic"> <param id="function">default</param> <param
id="type">python</param> </destination> <destination id="moab" runner="drmaa"
/> <destination id="local" runner="local" /> </destinations>
In my destinations.py script I point tools to the appropriate destination:
if tool_id.startswith('upload1'):
return JobDestination(id="local", runner="local")
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